He left the Enterprise at the end of 2364. His replacement, Geordi La Forge, did not consider him to be a very good engineer.

By 2375, he had been promoted to commander and was serving as second in command of the Starfleet Corps of Engineers under CaptainMontgomery Scott. Scott would often leave Lynch in de facto command of the S.C.E. while he left Headquarters for extended periods of time. Lynch took over the S.C.E. in August 2375 (Stardate 52612.6) when Scott went on inactive duty, but only on a temporary basis.

Lynch was regarded as a capable administrator by La Forge, but Scott would once sarcastically refer to him as "perfect for the job as a Klingon was for writing juicy romance novels", and Scott was often called upon in an advisory capacity to assist Lynch in making personnel decisions. By March 2376, Lynch had decided to resign as Corps liaison; he was replaced once again by Scott a month later. (SCEeBook: The Future Begins)